New Orders
by MissyLyssie
Summary: Sam receives some new orders. This is PG2. UPDATE! When I decided to continue this storyline, I kept it as the one story, rather than another separate one.
1. The Orders

A/N - Was writing in my diary at camp when this hit me. Wrote it in about 15 minutes. This one is most definitely PG2, as it will be set after my version of the SG-1 season 10 finale. So until I have written that, this may not fully make sense. Hope you like it anyway!

Sam's birthday as shown in 'Entity' is the 29th of December.

Please R&R!

**EDIT**: Just to let you guys know, I didn't use Phoenix as a ship name after the powers that be of Atlantis used it. I named this ship in September last year so I don't know if they'd already come up with theirs, but at the very least we hadn't heard any information about it until months after I wrote this.

* * *

"Working on your birthday, Carter?" Jack asked, wandering into her lab. Sam looked up and did a double take; just as she had done for the past few weeks since his change in appearance; before shrugging.

"Couldn't resist!" she replied, grinning, "Sir." She added.

"Bit cheeky there…" Jack warned playfully.

"Learnt from the best!" Sam returned with a grin. Jack smiled back at her before remembering the folder he held.

"Ah! Brought you this," he said, handing it to her. Sam took it and read the contents. As she read the smile on her face slipped slightly.

"Atlantis?" she asked.

"Yep," he responded with a nod.

"But I only just got back from there," Sam pointed out.

"The President thinks you're the best to look after things while Weir's incapacitated," he explained.

"But what about Sheppard? He knows the place and he's already there," she asked. Jack looked sceptical.

"With Elizabeth hurt? You think he'd be able to look after anything?" He asked.

"I guess…" Sam mused. Jack grinned once again.

"Means I get to promote you again," he prodded.

"Really?" Sam asked excitedly, looking up from the folder.

"Yeah. Full bird now… Almost catching me up!" Jack joked.

"Not likely…" Sam replied.

"Well, just think about this," Jack said, heading for the door.

"I will," Sam answered sincerely. Just before the he left the lab he turned again.

"Oh… did I mention that you get to command a ship to get to Atlantis first?" he said, before disappearing out the door. Sam frowned, looking down at the contents of the folder once again, searching… And found it.

'…_Command of Prometheus-class science vessel, the __**Phoenix**__.'_

Sam grinned, shaking her head.

"Prometheus class?" she mused out loud, before shaking her head again, "Betcha he named it too…" Placing the folder on the desk beside her, she went back to work, leaving it open to her next big adventure.

-tbc-

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A/N2 - I named the ship Phoenix because of the fact that the Prometheus was destroyed, and this ship of the same class has been made, just like the mythology of the Phoenix rising from the ashes. However, in the PG2 'universe' Prometheus class has been refitted as science vessels.


	2. Goodbyes

A/N - So... I didn't think I'd actually put any more chapters onto this, but I decided that, since the story was continuing on from what I wrote for chapter 1, I may as well post it here as further chapters.

In this chapter Sam says goodbye to her friends. And that's really all. Sorry if it seems boring it was needed to get from chapter 1 to the one after this.

Hope you enjoy!

Please read and review

* * *

Days later Sam was standing in the gateroom, newly promoted, having locked up her lab and packed her stuff for Atlantis. She found that handing experiments and ongoing projects off to the other scientists was easier than she expected. Saying goodbye to her friends for an indefinite period of time, on the other hand, was difficult.

She was standing with her back to the gate, her former team-mates standing almost in a semicircle in front of her, and General O'Neill on her left. To any SGC personnel who didn't know what was going on, it looked very much like she was moving off world. Which was true, in a way. Daniel was the first to step forward and hug her, a big smile on his face.

"You'll do great, Sam," he said reassuringly as he stepped back again. Cam scoffed from where he stood.

"Course she will, Jackson," he stated as he stepped forward and hugged her, "Have fun Sam, and don't open that til you're on Atlantis," he added, indicating a small box that sat on the top of her luggage. Sam grinned at him as he too stepped back. Unsurprisingly Teal'c hugged her next, actually picking her up off the ground.

"You will be greatly missed ColonelCarter," he stated as he set her down. Sam began to get a little teary eyed.

"Thank you Teal'c," she replied. Vala was a little more hesitant as she came to hug Sam.

"Keep an eye on the boys for me, will you?" Sam requested quietly and Vala grinned, any nervousness forgotten.

"Of course," she replied cheekily, "We **will** miss you," she added genuinely as she moved to stand back next to Teal'c. Daniel suddenly pulled something out of his pocket, his eyes wide.

"Oh! I was supposed to give this to you!" he stated, handing Sam an envelope, "It's from Cassie."

"Thanks," Sam said, a smile on her face. Turning, she regarded the man on her left. He had been strangely silent, just watching with a proud smile on his face. When she looked at him, he held out what she realised was her laptop case.

"You'll need this. It has the files for all the Atlantis personnel, as well as the ones for the latest additions," Jack explained. Sam smiled and took the offered bag, but was surprised when he hugged her too.

"You're ready for this Sam," he said honestly, squeezing her slightly.

"Thank you," she replied, purposely leaving off the 'sir'. He smiled at her as Walter called out from the control room.

"Ma'am, the Phoenix is ready to beam you up now," he said. Sam looked up to him and nodded.

"Thankyou. Tell them I'm ready," she replied. Looking back at her friends, she smiled, "Goodbye," she said as the familiar flash of the Asgard beam swept her away.

-tbc-


	3. Aboard the Phoenix

A/N - This chapter introduces the second, and certainly not the last, original character in the Project Generation 2 reality. His name is Wing Commander Nathan Baxter and he is the commander of the Phoenix. Or at least he will be, he just isn't yet. Nathan was created by my best friend, and so belongs to him.

Just a reminder, this Phoenix is **not** the same one as in SGA's 'The Last Man'. This ship is a Prometheus class. In the PG2 timeline Prometheus class ships have been redesigned as science ships.

This may be the last chapter for a short time, as I have some really big assignments that I have to work on. Just a warning!

Once again, I hope you enjoy the story.

Please read and review.

* * *

Arriving on board the Phoenix disoriented Sam and for a moment she looked down at the floor, waiting for her head to clear. Taking a better look around she noticed she was standing in the ring room; her stuff sitting off to one side.

"She's a beauty, isn't she ma'am?" a voice with a crisp British accent asked. Sam turned to see the almost-captain of the ship, Wing Commander Nathan Baxter standing to her right.

"Yes, she is," Sam replied.

"Welcome aboard the Phoenix, Colonel," Nathan then greeted formally, snapping off a salute. Sam returned it and Nathan directed some of his men to take her stuff to her quarters, before he and Sam headed out into the corridor.

"Thankyou. Are we about ready to head off?" she enquired.

"Not quite. Many of the personnel are still being beamed aboard. We should be away in about an hour at the most," Nathan replied, "In the meantime would you like to see around the ship?"

"Sure," Sam replied. Nathan led her around his ship, showing off the various modifications with pride, almost as though the Phoenix was his baby. Sam, although she had designed a fair amount of the Prometheus-class's systems and structure, was impressed by the modifications and improvements that had been made to the ship.

"Never thought I'd see a Prometheus-class fly again," Sam mused as they arrived on the bridge.

"I believe it was General O'Neill's idea, ma'am," Nathan stated as he looked over a report on of the crew had handed him. Sam looked at him in surprise.

"Really?" she asked. Nathan looked up at her briefly and nodded.

"That's what I was told," he replied. Sam nodded absently and then recalled something she had been curious about after receiving her orders.

"Did he name it too?" she asked. Nathan handed the report back to the crew member.

"I'm not sure," he said, turning back to her, "She was already named when I was assigned."

"Oh," Sam replied simply. Nathan grinned and looked around the bridge and out the front viewing port into space before returning his gaze to Sam as he was handed another report.

"All personnel are aboard, ma'am," he informed her after looking the report over, "Would you do us the honour of contacting Stargate Command?"

"Of course," Sam responded, giving a nod to the helmsman, "Stargate Command, this is the Phoenix."

"Go ahead Phoenix," Walter's voice replied.

"Request permission to depart," she stated confidently. For a moment there was silence, before a voice spoke, loud and clear, and very obviously full of pride.

"Permission granted Colonel," it responded. Sam grinned, easily recognising the voice.

"Thank you General," she said.

"Safe journey, Sam," Jack said, his voice slightly softer than usual.

"Thank you," Sam replied, matching his tone. There was another moment of silence before Jack spoke again, regaining his commanding tone.

"Colonel Carter, you and Wing Commander Baxter are to report as soon as you are able once you reach Atlantis. Understood?" he enquired, back to the task at hand.

"Acknowledged sir," Nathan replied crisply.

"Yes sir," Sam replied.

"Good. Have fun kids!" Jack stated in his usual flippant manner.

"Yes sir. Phoenix out," Sam replied, the tone of her voice matching the bright smile lighting up her face as she gave the next orders, "Helm, take us to Atlantis."

"Yes ma'am," the helmsman replied and the entire bridge crew stopped to watch as the hyperspace window formed and the Phoenix entered, big smiles all round. Sam sat down in the captain's chair and made a shipwide announcement.

"This is Colonel Carter. We are now en route to Atlantis," she announced, "As I am only in temporary command, I would like to take a moment to congratulate you all on making the Phoenix what it is. Well done, all of you," she stated, signing off. Sam looked to her right and saw Nathan standing behind her.

"You want the chair?" she asked with a grin.

"Not until I officially have command," he replied. Sam was surprised; she was used to people who would jump at the chance to sit in the captain's chair.

"She is your ship," Sam pointed out.

"Yes ma'am," Nathan agreed. Sam smiled and shook her head as she stood.

"I have personnel files for the latest additions to the expedition to go over, so I will be in my quarters if anyone needs me," she stated as she headed towards the door.

"Ma'am!" Nathan called out. Sam stopped and turned around.

"Yes?" she enquired. Nathan grinned at her.

"I'm sure the crew wouldn't mind if you had a look at the labs…" he suggested. Sam smiled back.

"I'm sure they wouldn't," she agreed, leaving the bridge.

-tbc-


	4. Arrival at Atlantis

A/N - I know it's taken a while, but here finally is the next chapter. It's taken this long due to the amount of assignments I have at the moment. Anyhow, here it is and I hope you enjoy it. This also includes the first time Brandyce Cameron (She was in An Encounter on the Pier) is introduced to any of the usual characters.

And so ends the first adventure for the crew of the Phoenix. I've enjoyed writing this, and I hope you've enjoyed reading it just as much.

Please read and review.

EDIT: You know, we really need a Stargate Crossover section, don't you think?

* * *

If Sam thought she would even be remotely bored during the short trip to Atlantis, she couldn't be any further from the truth. Borrowing the Odyssey's ZPM made the trip shorter, but she still had enough time to not only go over the personnel files she had on her laptop, but also to visit the labs onboard the ship. Nathan had been right in assuming that the scientists would be only too happy to show her around, and it wasn't only the physicists, scientists from every department showed off their labs proudly. She'd had a tour of the ship when she'd first come aboard, but the scientists proved themselves by giving her a closer examination of everything.

All too soon they arrived at the new planet Atlantis had been settled on and Sam, sitting for the last time in the captain's chair, on the bridge, marvelled at its similarity to Lantea, as they came into orbit around it. Standing up, she looked around the bridge before nodding at the helmsman to begin her farewell to the crew

"If I may have your attention for a moment, before I leave I would like to thank you for being one of the best crews a commander could have, however short my command has been," she began, looking around at the bridge crew as she spoke and noticed Nathan moving closer to where she stood.

"But now, as per my orders, I hand full command of the Phoenix over to Wing Commander Nathan Baxter," she continued formally, smiling as Nathan sat down in the captain's chair.

"I hope that he, and this entire crew, make many discoveries and have many adventures, though I hope you all stay out of trouble if you can," Sam continued, pausing only to wait out the crew's scattered laughter.

"I wish you all good luck," Sam finished, smiling as she heard applause. Walking over to the captain's chair, she put her hand on Nathan's shoulder.

"Good luck and safe journeys, Nathan," she said.

"Thank you ma'am," Nathan replied, smiling up at her. Sam smiled and walked off the bridge towards her temporary quarters to get the last of her bags, it was only her laptop case and the small box Cam had given her left, the other things had been beamed down already with the bulk of the new additions luggage.

As she headed down the corridors to the ring room, a voice called out from behind her. Turning she saw a petite dark haired woman heading towards her, pulling a small suitcase. Sam stopped and smiled, not entirely sure who the woman was.

"Sorry for delaying you, Colonel," the woman apologised.

"No, it's fine," Sam replied, still wondering which new addition this was. The woman must have sensed her confusion, because she introduced herself with a grin.

"Doctor Brandyce Cameron."

"Oh! You're the physical therapist Colonel Sheppard requested," Sam realised. Brandi nodded.

"Yes ma'am," she replied as they entered the ring room and joined the rest of the personnel to be beamed down. Nathan was standing among them, and smiled when he saw Sam and Brandi arrive. Though, Sam noted, it wasn't at her. Looking around, he made sure everyone was there, before turning to the Lieutenant at the console beside him.

"Go ahead Lieutenant," he stated. The Lieutenant nodded and made some adjustments to the controls. The personnel immediately felt the familiar tingle of the Asgard beam before they were suddenly in Atlantis.

A couple of Atlantis's security personnel, obviously directed by Colonel Sheppard, headed over to direct the new arrivals to their proper places, leaving only Sam and Nathan standing in the Gateroom.

Looking over to the stairs, they saw John Sheppard walking over to them. As soon as he reached them Nathan snapped off a salute, which Sam copied and John returned.

"Colonel Carter, Wing Commander Baxter. Welcome to Atlantis," he greeted.

-fin-


End file.
